DiffDock

5-30 minutesPaperCodeNeed >5GB

Protein-ligand docking with diffusion models

Readiness

Readiness: Need >5GB
Smoke: passed
Artifacts: passed
Production: need_gt5gb_diffdock_source_models_staged_sif_pull_failed_retry_pending
Storage: >5
Strategy: large shared SIF/database/model bundle phase
Next: Clean or relocate failed Singularity/OCI cache if safe, retry DiffDock SIF pull or build from upstream image on a more stable connection, then run bundled protein_ligand_example.csv with samples_per_complex=1 through Slurm/API and verify ranked SDF/confidence artifacts.

large model weights, structure DBs, docking/MD assets, or GPU stack likely >5GB 2026-07-17T01:36:00+08:00 SOP Need >5GB next-10 audit: remains Need >5GB. Runner audit is not_configured and existing object-store job used generic-smoke. Backend inventory found no DiffDock repo/SIF/checkpoints or docking test assets under the current shared root; needs real DiffDock SIF/checkpoints and pose/scores smoke. 2026-07-19T23:00:00+08:00 SOP Need >5GB active install continuation: Official DiffDock source staged on backend at /media/nik/seagate_nik/bio_server/repos/diffdock (240MB). Public diffdock_models.zip downloaded to /media/nik/seagate_nik/bio_server/cache/diffdock/diffdock_models.zip, 129,825,226 bytes. Singularity pull/conversion for docker://rbgcsail/diffdock:latest started in background; log /media/nik/seagate_nik/bio_server/logs/diffdock/stage_diffdock_20260719.log, PID file /media/nik/seagate_nik/bio_server/logs/diffdock/stage_diffdock_20260719.pid. No inference benchmark yet. 2026-07-20T22:20:00+08:00 SOP Need >5GB active install continuation: DiffDock source remained staged at /media/nik/seagate_nik/bio_server/repos/diffdock (240MB) and diffdock_models.zip 129,825,226 bytes was downloaded to /media/nik/seagate_nik/bio_server/cache/diffdock. Singularity pull of docker://rbgcsail/diffdock:latest failed during OCI-to-SIF conversion with `stream error: stream ID 31; INTERNAL_ERROR; received from peer`. No DiffDock SIF or inference benchmark exists yet. Disk was down to 19GB free; /home/nik/.singularity cache was 7.0GB and mamba/cache dirs are large. 2026-07-20T22:45:00+08:00 SOP Need >5GB continuation: cleaned failed Singularity OCI cache and micromamba package cache, restoring free disk from 19GB to 37GB. DiffDock remains Need >5GB because docker://rbgcsail/diffdock:latest SIF conversion previously failed with OCI stream INTERNAL_ERROR; no retry started while RFdiffusion SIF pull is running.